General project set-up

# Load libraries and sources required to run the script
    library(tidyverse)
    library(ggthemes)
    library(lmerTest)
    library(emmeans)
    library(multcomp)
    library(effects)

# Default ggplot settings

    Fill.colour<-scale_colour_manual(values = c("black", "gray70", "gray35"))

    ggthe_bw<-theme(plot.background=element_blank(),
          panel.grid.major.y = element_blank(),
          panel.grid.major.x = element_blank(),
          panel.grid.minor.x = element_blank(),
          panel.grid.minor.y = element_blank(),
          legend.box.background = element_rect(),
          panel.background =element_rect(fill = NA, color = "black")
          )+
    theme_bw()

Data exploration

1. Get the files with all the YII by species

# Acer
    YII.Acer<-read.csv("YII_Data/YII_Nutrients_Acer.csv", header = T)
      YII.Acer$Fragment<-as.character(YII.Acer$Fragment)  # Fragment ID to character
      YII.Acer<-subset(YII.Acer, Colony!="F")
      YII.Acer<-subset(YII.Acer , Treatment!="Dead")
    ## Genotype information
      MOTE<-read.csv("Genotypes_mote.csv", header = TRUE)
      YII.Acer<-merge(YII.Acer, MOTE, by="Colony", all.x=TRUE)

# Ofav    
    YII.Ofav<-read.csv("YII_Data/YII_Nutrients_Ofav.csv")
      YII.Ofav$Colony<-factor(as.character(YII.Ofav$Colony), 
                            levels=c("31","6","20","34"))  # D dominance order
      YII.Ofav$Genotype<-paste("Ofav", YII.Ofav$Colony, sep = "_")

# Ssid      
    YII.Ssid<-read.csv("YII_Data/YII_Nutrients_Ssid.csv")
      YII.Ssid$Colony<-factor(as.character(YII.Ssid$Colony), 
                                 levels=c("30","20","24","28","22","23","27") )  # D dominance order
      YII.Ssid$Genotype<-paste("Ssid", YII.Ssid$Colony, sep = "_")
    
# Pool all species the data
      YII.data<-dplyr::bind_rows(list(YII.Acer,YII.Ofav,YII.Ssid))
      YII.data<-YII.data[,-1]
      summary(YII.data)
##       Time           Date               Spp              Fragment        
##  Min.   : 0.00   Length:6018        Length:6018        Length:6018       
##  1st Qu.: 6.00   Class :character   Class :character   Class :character  
##  Median :11.00   Mode  :character   Mode  :character   Mode  :character  
##  Mean   :11.13                                                           
##  3rd Qu.:16.00                                                           
##  Max.   :23.00                                                           
##   Treatment          Replicate              YII            Sample         
##  Length:6018        Length:6018        Min.   :0.0000   Length:6018       
##  Class :character   Class :character   1st Qu.:0.4420   Class :character  
##  Mode  :character   Mode  :character   Median :0.5030   Mode  :character  
##                                        Mean   :0.4989                     
##                                        3rd Qu.:0.5720                     
##                                        Max.   :0.6870                     
##    Genotype        
##  Length:6018       
##  Class :character  
##  Mode  :character  
##                    
##                    
## 
# Organize data type
      YII.data$Date<-as.Date(YII.data$Date, "%Y-%m-%d")
      YII.data$Days<-(as.numeric(YII.data$Date) -17485)
      
      YII.data$Spp <- as.factor(YII.data$Spp)
      YII.data$Treatment[YII.data$Treatment == "Control"] <- "Ambient"
      YII.data$Treatment[YII.data$Treatment == "NP"] <- "N+P"
      YII.data$Treatment <- as.factor(YII.data$Treatment)
      YII.data$Genotype<-factor(as.character(YII.data$Genotype), 
                             levels=c("Acer_07","Acer_08","Acer_31",
                                      "Acer_48","Acer_50","Acer_62", 
                             "Ofav_31","Ofav_6","Ofav_20","Ofav_34", 
                             "Ssid_30","Ssid_20","Ssid_24",
                             "Ssid_28","Ssid_22","Ssid_23","Ssid_27"))  # D dominance order
      YII.data$Fragment <- paste(YII.data$Spp, YII.data$Fragment, sep = "_")
      
# Check the data
      str(YII.data)
## 'data.frame':    6018 obs. of  10 variables:
##  $ Time     : int  3 5 3 2 2 6 11 1 7 2 ...
##  $ Date     : Date, format: "2017-10-19" "2017-11-16" ...
##  $ Spp      : Factor w/ 3 levels "A.cer","O.fav",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ Fragment : chr  "A.cer_284" "A.cer_180" "A.cer_277" "A.cer_180" ...
##  $ Treatment: Factor w/ 3 levels "Ambient","N",..: 1 2 1 2 1 3 1 3 1 1 ...
##  $ Replicate: chr  "R2" "R2" "R2" "R2" ...
##  $ YII      : num  0.552 0.607 0.56 0.53 0.533 0.648 0.594 0.479 0.633 0.517 ...
##  $ Sample   : chr  "2017-10-19_284" "2017-11-16_180" "2017-10-19_277" "2017-10-10_180" ...
##  $ Genotype : Factor w/ 17 levels "Acer_07","Acer_08",..: 4 4 4 4 4 4 4 4 4 4 ...
##  $ Days     : num  -27 1 -27 -36 -36 8 65 -77 14 -36 ...
      summary(YII.data)
##       Time            Date               Spp         Fragment        
##  Min.   : 0.00   Min.   :2017-07-26   A.cer:2280   Length:6018       
##  1st Qu.: 6.00   1st Qu.:2017-11-29   O.fav:1051   Class :character  
##  Median :11.00   Median :2018-01-19   S.sid:2687   Mode  :character  
##  Mean   :11.13   Mean   :2018-01-06                                  
##  3rd Qu.:16.00   3rd Qu.:2018-02-15                                  
##  Max.   :23.00   Max.   :2018-04-20                                  
##                                                                      
##    Treatment     Replicate              YII            Sample         
##  Ambient:2096   Length:6018        Min.   :0.0000   Length:6018       
##  N      :1973   Class :character   1st Qu.:0.4420   Class :character  
##  N+P    :1949   Mode  :character   Median :0.5030   Mode  :character  
##                                    Mean   :0.4989                     
##                                    3rd Qu.:0.5720                     
##                                    Max.   :0.6870                     
##                                                                       
##     Genotype         Days        
##  Acer_62: 577   Min.   :-112.00  
##  Acer_48: 569   1st Qu.:  14.00  
##  Acer_07: 462   Median :  65.00  
##  Ssid_20: 402   Mean   :  52.41  
##  Ssid_23: 402   3rd Qu.:  92.00  
##  Ssid_30: 400   Max.   : 156.00  
##  (Other):3206
      summary(YII.data$Genotype)
## Acer_07 Acer_08 Acer_31 Acer_48 Acer_50 Acer_62 Ofav_31  Ofav_6 Ofav_20 
##     462     145     304     569     223     577     213     275     284 
## Ofav_34 Ssid_30 Ssid_20 Ssid_24 Ssid_28 Ssid_22 Ssid_23 Ssid_27 
##     279     400     402     362     332     389     402     400
    # Remove baseline values
      YII.data<-subset(YII.data, Days>-1)
    # Remove recovery values
      YII.data<-subset(YII.data, Days<112)
    
    # YII.Wide<- reshape(YII.data, idvar = "Fragment", timevar = "Days", direction = "wide")
      
# Subset data before heat stress (Only nutrients)
      YII.nutrients<-subset(YII.data, Days<80)

2. Exploratory graphs

All time points (nutrients + heat stress)

  • Colony (Genotype) differences
YII_Colony<- ggplot(YII.data, aes (Days, YII, colour=Genotype)) +
        stat_summary(fun.data = "mean_cl_boot",geom = "errorbar", width = 0.5)+
        stat_summary(fun.y=mean, geom="line", alpha=0.6) +   theme_bw()
      YII_Colony + ylim(0.0, 0.65) + facet_grid (Spp~Treatment)

      YII_Fragment<- ggplot(YII.data, aes (Days, YII, colour=factor(Fragment))) +
        stat_summary(fun.y=mean, geom="line", alpha=0.6) +  
        theme_bw() + theme(legend.position = "none")
      YII_Fragment + ylim(0.0, 0.65) + facet_grid (Spp~Treatment)

      YII_Frag_Gen<- ggplot(YII.data, aes (Days, YII, colour=Genotype, shape=Fragment)) +
        stat_summary(fun.y=mean, geom="line", alpha=0.5) +  
        theme_bw() + theme(legend.position = "bottom",
                           legend.title = element_blank())
      YII_Frag_Gen + ylim(0.0, 0.65) + facet_grid (Spp~Treatment)

  • Treatment differences
YII_Treat<- ggplot(YII.data, aes (Days, YII, colour=Treatment)) +
        stat_summary(fun.data = "mean_cl_boot",geom = "errorbar", width = 0.2, position = position_dodge(1) )+
        stat_summary(fun.y=mean, geom="line") + ggthe_bw +
        theme(legend.position="bottom",
              strip.background = element_rect(fill="white"))+
        scale_y_continuous(limits = c(0.2, 0.7),
                           breaks = seq(0.2, 0.6, 0.1),  
                           expand = c(0, 0),
                           name=("Fv/Fm")) +
        scale_x_continuous(name="Days in the experiment",
                           limits = c(-1,113),
                           breaks = seq(0, 113, 15),  
                           expand = c(0, 0))+
        annotate("rect", xmin= 2, xmax = 86,
                 ymin = 0.2, ymax =0.3, fill="blue", alpha = .05)+
        annotate("rect", xmin= 72, xmax = 85,
                 ymin = 0.2, ymax =0.7, fill="orange", alpha = .05)+
        annotate("rect", xmin= 85, xmax = 113,
                 ymin = 0.2, ymax =0.7, fill="red", alpha = .05) + facet_grid (Spp~.)
      YII_Treat

Figure 3

YII_Treat_BW<- ggplot(YII.data, aes (Days, YII, colour=factor(Treatment), shape=factor(Treatment))) +
        ggthe_bw + Fill.colour+
        stat_summary(fun.data = "mean_cl_boot",geom = "errorbar", width = 1, position = position_dodge(1) )+
        stat_summary(fun.y=mean, geom="line", position = position_dodge(1), linetype=1, alpha=0.8) + 
         stat_summary(fun.y=mean, geom="point", size =1,
                   position=position_dodge(width=1))  +
        theme(legend.position="bottom", 
              legend.title = element_blank(),
              strip.background = element_rect(fill="white"))+
        scale_y_continuous(limits = c(0.1, 0.7),
                           breaks = seq(0.1, 0.6, 0.1),  
                           expand = c(0, 0),
                           name=expression(~italic("Fv / Fm"))) +
        scale_x_continuous(name="Days in the experiment",
                           limits = c(-1,113),
                           breaks = seq(0, 113, 15),  
                           expand = c(0, 0))+
        annotate("segment", x = 2, xend = 91, y = 0.12, yend = 0.13,
                  colour = "gray90", linetype=2)+
        annotate("segment", x = 79, xend = 91, y = 0.12, yend = 0.25,
                  colour = "gray90", linetype=4)+
        annotate("segment", x = 91, xend = 110, y = 0.25, yend = 0.25,
                  colour = "gray90", linetype=3)
        
      
      Figure3<-YII_Treat_BW +facet_grid (Spp~.)+
        annotate("text", x = 45, y = 0.2, label = "Nutrients", size=3)+
        annotate("text", x = 99, y = 0.2, label = "Bleaching", size=3)
Figure3

#ggsave(file="5.3_YII_Treat.svg", plot=YII_Treat, width=4.0, height=6)

Figure 3 Supplemantary: Treatment effect by genotype

Figure3b<-YII_Treat_BW +facet_wrap (~Genotype, ncol = 6)
Figure3b

#ggsave(file="5.3_YII_Treat.svg", plot=YII_Treat, width=4.0, height=6)

YII GLMs

#Time as a factor, not as int
      str(YII.data)
## 'data.frame':    5016 obs. of  10 variables:
##  $ Time     : int  5 6 11 7 11 7 9 7 8 6 ...
##  $ Date     : Date, format: "2017-11-16" "2017-11-23" ...
##  $ Spp      : Factor w/ 3 levels "A.cer","O.fav",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ Fragment : chr  "A.cer_180" "A.cer_283" "A.cer_290" "A.cer_182" ...
##  $ Treatment: Factor w/ 3 levels "Ambient","N",..: 2 3 1 1 3 2 1 2 1 3 ...
##  $ Replicate: chr  "R2" "R1" "R2" "R1" ...
##  $ YII      : num  0.607 0.648 0.594 0.633 0.621 0.636 0.63 0.637 0.638 0.637 ...
##  $ Sample   : chr  "2017-11-16_180" "2017-11-23_283" "2018-01-19_290" "2017-11-29_182" ...
##  $ Genotype : Factor w/ 17 levels "Acer_07","Acer_08",..: 4 4 4 4 4 4 4 4 4 4 ...
##  $ Days     : num  1 8 65 14 65 14 28 14 21 8 ...
      YII.data$DaysF<-as.factor(YII.data$Days)

# All spp together
      LME1<-lmer(YII ~ Treatment * DaysF * Spp + (1|Genotype),
                REML=TRUE, data=YII.data, na.action=na.omit)
       lmerTest::step (LME1)
## Backward reduced random-effect table:
## 
##                Eliminated npar logLik    AIC    LRT Df Pr(>Chisq)    
## <none>                     154 8706.6 -17105                         
## (1 | Genotype)          0  153 8298.0 -16290 817.37  1  < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Backward reduced fixed-effect table:
## Degrees of freedom method: Satterthwaite 
## 
##                     Eliminated Sum Sq  Mean Sq NumDF  DenDF F value
## Treatment:DaysF:Spp          0 1.2863 0.020417    63 4850.1  14.076
##                        Pr(>F)    
## Treatment:DaysF:Spp < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Model found:
## YII ~ Treatment * DaysF * Spp + (1 | Genotype)
       drop1(LME1, test = "Chisq")
## Single term deletions using Satterthwaite's method:
## 
## Model:
## YII ~ Treatment * DaysF * Spp + (1 | Genotype)
##                     Sum Sq  Mean Sq NumDF  DenDF F value    Pr(>F)    
## Treatment:DaysF:Spp 1.2863 0.020417    63 4850.1  14.076 < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
       summary(LME1)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: YII ~ Treatment * DaysF * Spp + (1 | Genotype)
##    Data: YII.data
## 
## REML criterion at convergence: -17413.3
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -9.6697 -0.4535  0.0540  0.5460  3.4938 
## 
## Random effects:
##  Groups   Name        Variance  Std.Dev.
##  Genotype (Intercept) 0.0003385 0.01840 
##  Residual             0.0014505 0.03808 
## Number of obs: 5016, groups:  Genotype, 17
## 
## Fixed effects:
##                                  Estimate Std. Error         df t value
## (Intercept)                     6.122e-01  9.690e-03  3.756e+01  63.171
## TreatmentN                     -1.124e-02  8.520e-03  4.850e+03  -1.320
## TreatmentN+P                   -6.996e-03  8.572e-03  4.850e+03  -0.816
## DaysF8                         -1.641e-03  8.625e-03  4.850e+03  -0.190
## DaysF14                         6.462e-03  8.625e-03  4.850e+03   0.749
## DaysF21                        -6.231e-03  8.625e-03  4.850e+03  -0.722
## DaysF28                        -1.144e-02  8.625e-03  4.850e+03  -1.326
## DaysF49                        -3.321e-02  8.625e-03  4.850e+03  -3.850
## DaysF65                        -4.377e-02  8.625e-03  4.850e+03  -5.075
## DaysF71                        -4.256e-02  8.625e-03  4.850e+03  -4.935
## DaysF76                        -5.182e-02  8.625e-03  4.850e+03  -6.009
## DaysF84                        -4.619e-02  9.084e-03  4.850e+03  -5.084
## DaysF89                        -6.447e-02  9.084e-03  4.850e+03  -7.097
## DaysF92                        -5.344e-02  9.084e-03  4.850e+03  -5.882
## DaysF96                        -5.322e-02  9.084e-03  4.850e+03  -5.858
## DaysF99                        -7.894e-02  9.084e-03  4.850e+03  -8.689
## DaysF103                       -9.828e-02  9.084e-03  4.850e+03 -10.819
## DaysF106                       -1.152e-01  9.084e-03  4.850e+03 -12.680
## DaysF110                       -2.124e-01  9.084e-03  4.850e+03 -23.381
## SppO.fav                       -1.057e-01  1.546e-02  3.892e+01  -6.840
## SppS.sid                       -1.454e-01  1.300e-02  3.534e+01 -11.182
## TreatmentN:DaysF8               2.749e-02  1.205e-02  4.850e+03   2.282
## TreatmentN+P:DaysF8             2.182e-02  1.212e-02  4.850e+03   1.800
## TreatmentN:DaysF14              8.197e-03  1.205e-02  4.850e+03   0.680
## TreatmentN+P:DaysF14            1.586e-02  1.212e-02  4.850e+03   1.309
## TreatmentN:DaysF21              4.433e-02  1.205e-02  4.850e+03   3.680
## TreatmentN+P:DaysF21            2.751e-02  1.212e-02  4.850e+03   2.269
## TreatmentN:DaysF28              4.173e-02  1.205e-02  4.850e+03   3.464
## TreatmentN+P:DaysF28            4.296e-02  1.212e-02  4.850e+03   3.544
## TreatmentN:DaysF49              6.755e-02  1.205e-02  4.850e+03   5.607
## TreatmentN+P:DaysF49            6.271e-02  1.212e-02  4.850e+03   5.173
## TreatmentN:DaysF65              4.211e-02  1.205e-02  4.850e+03   3.495
## TreatmentN+P:DaysF65            5.670e-02  1.216e-02  4.850e+03   4.663
## TreatmentN:DaysF71              5.384e-02  1.216e-02  4.850e+03   4.426
## TreatmentN+P:DaysF71            2.865e-02  1.216e-02  4.850e+03   2.356
## TreatmentN:DaysF76              5.275e-02  1.221e-02  4.850e+03   4.321
## TreatmentN+P:DaysF76            3.944e-02  1.216e-02  4.850e+03   3.244
## TreatmentN:DaysF84              3.662e-02  1.303e-02  4.850e+03   2.811
## TreatmentN+P:DaysF84            4.123e-02  1.293e-02  4.850e+03   3.189
## TreatmentN:DaysF89              3.895e-02  1.310e-02  4.850e+03   2.972
## TreatmentN+P:DaysF89            3.061e-02  1.293e-02  4.850e+03   2.368
## TreatmentN:DaysF92             -4.387e-03  1.346e-02  4.850e+03  -0.326
## TreatmentN+P:DaysF92            2.373e-02  1.314e-02  4.850e+03   1.806
## TreatmentN:DaysF96             -4.963e-02  1.396e-02  4.851e+03  -3.555
## TreatmentN+P:DaysF96           -1.925e-02  1.399e-02  4.850e+03  -1.377
## TreatmentN:DaysF99             -1.179e-01  1.428e-02  4.851e+03  -8.257
## TreatmentN+P:DaysF99           -4.192e-02  1.431e-02  4.851e+03  -2.929
## TreatmentN:DaysF103            -1.128e-01  1.492e-02  4.851e+03  -7.558
## TreatmentN+P:DaysF103          -9.829e-02  1.450e-02  4.851e+03  -6.779
## TreatmentN:DaysF106            -1.806e-01  1.674e-02  4.851e+03 -10.790
## TreatmentN+P:DaysF106          -1.439e-01  1.551e-02  4.851e+03  -9.277
## TreatmentN:DaysF110             6.492e-02  1.122e-02  4.850e+03   5.789
## TreatmentN+P:DaysF110          -1.302e-01  2.024e-02  4.850e+03  -6.435
## TreatmentN:SppO.fav             1.945e-02  1.391e-02  4.850e+03   1.399
## TreatmentN+P:SppO.fav           1.870e-02  1.394e-02  4.850e+03   1.342
## TreatmentN:SppS.sid            -1.402e-02  1.122e-02  4.850e+03  -1.250
## TreatmentN+P:SppS.sid          -4.073e-04  1.130e-02  4.850e+03  -0.036
## DaysF8:SppO.fav                -1.219e-02  1.397e-02  4.850e+03  -0.873
## DaysF14:SppO.fav                3.050e-02  1.397e-02  4.850e+03   2.182
## DaysF21:SppO.fav               -2.289e-02  1.397e-02  4.850e+03  -1.638
## DaysF28:SppO.fav               -2.314e-03  1.397e-02  4.850e+03  -0.166
## DaysF49:SppO.fav               -1.959e-02  1.397e-02  4.850e+03  -1.402
## DaysF65:SppO.fav                3.827e-02  1.397e-02  4.850e+03   2.739
## DaysF71:SppO.fav                3.856e-03  1.397e-02  4.850e+03   0.276
## DaysF76:SppO.fav                1.278e-02  1.397e-02  4.850e+03   0.915
## DaysF84:SppO.fav                3.108e-02  1.528e-02  4.850e+03   2.034
## DaysF89:SppO.fav                3.480e-02  1.528e-02  4.850e+03   2.277
## DaysF92:SppO.fav                6.172e-02  1.548e-02  4.850e+03   3.987
## DaysF96:SppO.fav               -2.083e-02  1.548e-02  4.850e+03  -1.345
## DaysF99:SppO.fav                3.557e-03  1.548e-02  4.850e+03   0.230
## DaysF103:SppO.fav               2.501e-03  1.548e-02  4.850e+03   0.162
## DaysF106:SppO.fav              -1.458e-02  1.571e-02  4.850e+03  -0.928
## DaysF110:SppO.fav               1.197e-01  1.626e-02  4.850e+03   7.360
## DaysF8:SppS.sid                 2.929e-02  1.132e-02  4.850e+03   2.588
## DaysF14:SppS.sid                7.778e-02  1.132e-02  4.850e+03   6.872
## DaysF21:SppS.sid                2.895e-02  1.132e-02  4.850e+03   2.558
## DaysF28:SppS.sid                7.507e-02  1.132e-02  4.850e+03   6.632
## DaysF49:SppS.sid                5.378e-02  1.132e-02  4.850e+03   4.752
## DaysF65:SppS.sid                6.916e-02  1.134e-02  4.850e+03   6.099
## DaysF71:SppS.sid                5.727e-02  1.134e-02  4.850e+03   5.050
## DaysF76:SppS.sid                6.734e-02  1.134e-02  4.850e+03   5.938
## DaysF84:SppS.sid                4.841e-02  1.211e-02  4.850e+03   3.999
## DaysF89:SppS.sid                3.723e-02  1.211e-02  4.850e+03   3.075
## DaysF92:SppS.sid                3.507e-02  1.211e-02  4.850e+03   2.897
## DaysF96:SppS.sid               -3.794e-02  1.211e-02  4.850e+03  -3.134
## DaysF99:SppS.sid               -1.238e-02  1.211e-02  4.850e+03  -1.022
## DaysF103:SppS.sid              -1.519e-02  1.211e-02  4.850e+03  -1.254
## DaysF106:SppS.sid              -9.407e-03  1.211e-02  4.850e+03  -0.777
## DaysF110:SppS.sid               1.168e-01  1.211e-02  4.850e+03   9.648
## TreatmentN:DaysF8:SppO.fav     -2.412e-02  1.967e-02  4.850e+03  -1.226
## TreatmentN+P:DaysF8:SppO.fav   -2.623e-02  1.971e-02  4.850e+03  -1.331
## TreatmentN:DaysF14:SppO.fav    -2.474e-02  1.967e-02  4.850e+03  -1.258
## TreatmentN+P:DaysF14:SppO.fav  -2.141e-02  1.971e-02  4.850e+03  -1.086
## TreatmentN:DaysF21:SppO.fav    -4.079e-02  1.967e-02  4.850e+03  -2.074
## TreatmentN+P:DaysF21:SppO.fav  -2.167e-02  1.971e-02  4.850e+03  -1.099
## TreatmentN:DaysF28:SppO.fav    -2.273e-02  1.967e-02  4.850e+03  -1.156
## TreatmentN+P:DaysF28:SppO.fav  -9.669e-03  1.971e-02  4.850e+03  -0.490
## TreatmentN:DaysF49:SppO.fav    -3.638e-02  1.967e-02  4.850e+03  -1.850
## TreatmentN+P:DaysF49:SppO.fav  -2.404e-02  1.971e-02  4.850e+03  -1.219
## TreatmentN:DaysF65:SppO.fav    -7.082e-02  1.967e-02  4.850e+03  -3.600
## TreatmentN+P:DaysF65:SppO.fav  -5.528e-02  1.974e-02  4.850e+03  -2.801
## TreatmentN:DaysF71:SppO.fav    -5.492e-02  1.974e-02  4.850e+03  -2.782
## TreatmentN+P:DaysF71:SppO.fav  -6.173e-02  1.974e-02  4.850e+03  -3.127
## TreatmentN:DaysF76:SppO.fav    -5.546e-02  1.977e-02  4.850e+03  -2.806
## TreatmentN+P:DaysF76:SppO.fav  -4.890e-02  1.974e-02  4.850e+03  -2.477
## TreatmentN:DaysF84:SppO.fav    -4.521e-02  2.172e-02  4.850e+03  -2.081
## TreatmentN+P:DaysF84:SppO.fav  -4.250e-02  2.166e-02  4.850e+03  -1.962
## TreatmentN:DaysF89:SppO.fav    -6.400e-02  2.191e-02  4.850e+03  -2.921
## TreatmentN+P:DaysF89:SppO.fav  -3.270e-02  2.166e-02  4.850e+03  -1.509
## TreatmentN:DaysF92:SppO.fav    -2.266e-02  2.242e-02  4.850e+03  -1.011
## TreatmentN+P:DaysF92:SppO.fav  -5.863e-02  2.206e-02  4.850e+03  -2.657
## TreatmentN:DaysF96:SppO.fav     4.542e-02  2.272e-02  4.850e+03   1.999
## TreatmentN+P:DaysF96:SppO.fav   2.297e-02  2.273e-02  4.850e+03   1.010
## TreatmentN:DaysF99:SppO.fav     8.656e-02  2.292e-02  4.850e+03   3.777
## TreatmentN+P:DaysF99:SppO.fav   3.442e-02  2.355e-02  4.850e+03   1.461
## TreatmentN:DaysF103:SppO.fav    8.987e-02  2.332e-02  4.850e+03   3.854
## TreatmentN+P:DaysF103:SppO.fav  1.016e-01  2.367e-02  4.850e+03   4.291
## TreatmentN:DaysF106:SppO.fav    1.431e-01  2.483e-02  4.850e+03   5.765
## TreatmentN+P:DaysF106:SppO.fav  1.174e-01  2.444e-02  4.850e+03   4.805
## TreatmentN:DaysF110:SppO.fav   -1.363e-01  2.210e-02  4.850e+03  -6.167
## TreatmentN+P:DaysF110:SppO.fav  9.427e-02  2.799e-02  4.850e+03   3.368
## TreatmentN:DaysF8:SppS.sid      1.403e-03  1.586e-02  4.850e+03   0.088
## TreatmentN+P:DaysF8:SppS.sid    1.772e-02  1.598e-02  4.850e+03   1.109
## TreatmentN:DaysF14:SppS.sid     1.325e-02  1.586e-02  4.850e+03   0.836
## TreatmentN+P:DaysF14:SppS.sid  -4.293e-03  1.598e-02  4.850e+03  -0.269
## TreatmentN:DaysF21:SppS.sid    -2.832e-03  1.586e-02  4.850e+03  -0.179
## TreatmentN+P:DaysF21:SppS.sid   1.396e-02  1.598e-02  4.850e+03   0.874
## TreatmentN:DaysF28:SppS.sid     4.460e-03  1.586e-02  4.850e+03   0.281
## TreatmentN+P:DaysF28:SppS.sid  -1.716e-02  1.598e-02  4.850e+03  -1.074
## TreatmentN:DaysF49:SppS.sid    -4.065e-02  1.586e-02  4.850e+03  -2.563
## TreatmentN+P:DaysF49:SppS.sid  -5.656e-02  1.598e-02  4.850e+03  -3.540
## TreatmentN:DaysF65:SppS.sid    -6.296e-02  1.588e-02  4.850e+03  -3.965
## TreatmentN+P:DaysF65:SppS.sid  -5.925e-02  1.604e-02  4.850e+03  -3.694
## TreatmentN:DaysF71:SppS.sid    -4.964e-02  1.597e-02  4.850e+03  -3.109
## TreatmentN+P:DaysF71:SppS.sid  -2.798e-02  1.603e-02  4.850e+03  -1.746
## TreatmentN:DaysF76:SppS.sid    -4.729e-02  1.600e-02  4.850e+03  -2.956
## TreatmentN+P:DaysF76:SppS.sid  -4.181e-02  1.603e-02  4.850e+03  -2.609
## TreatmentN:DaysF84:SppS.sid    -4.825e-02  1.719e-02  4.850e+03  -2.806
## TreatmentN+P:DaysF84:SppS.sid  -3.355e-02  1.717e-02  4.850e+03  -1.954
## TreatmentN:DaysF89:SppS.sid    -2.767e-02  1.725e-02  4.850e+03  -1.604
## TreatmentN+P:DaysF89:SppS.sid  -3.895e-02  1.717e-02  4.850e+03  -2.268
## TreatmentN:DaysF92:SppS.sid     3.091e-02  1.752e-02  4.850e+03   1.764
## TreatmentN+P:DaysF92:SppS.sid  -1.743e-02  1.733e-02  4.850e+03  -1.006
## TreatmentN:DaysF96:SppS.sid     1.169e-01  1.791e-02  4.850e+03   6.529
## TreatmentN+P:DaysF96:SppS.sid   4.420e-02  1.798e-02  4.850e+03   2.458
## TreatmentN:DaysF99:SppS.sid     1.772e-01  1.816e-02  4.850e+03   9.758
## TreatmentN+P:DaysF99:SppS.sid   5.259e-02  1.824e-02  4.850e+03   2.884
## TreatmentN:DaysF103:SppS.sid    1.909e-01  1.867e-02  4.851e+03  10.229
## TreatmentN+P:DaysF103:SppS.sid  1.203e-01  1.838e-02  4.850e+03   6.542
## TreatmentN:DaysF106:SppS.sid    2.355e-01  2.015e-02  4.850e+03  11.686
## TreatmentN+P:DaysF106:SppS.sid  1.514e-01  1.919e-02  4.850e+03   7.892
## TreatmentN+P:DaysF110:SppS.sid  1.491e-01  2.318e-02  4.850e+03   6.431
##                                Pr(>|t|)    
## (Intercept)                     < 2e-16 ***
## TreatmentN                     0.186973    
## TreatmentN+P                   0.414421    
## DaysF8                         0.849102    
## DaysF14                        0.453770    
## DaysF21                        0.470054    
## DaysF28                        0.184911    
## DaysF49                        0.000120 ***
## DaysF65                        4.02e-07 ***
## DaysF71                        8.27e-07 ***
## DaysF76                        2.01e-09 ***
## DaysF84                        3.83e-07 ***
## DaysF89                        1.46e-12 ***
## DaysF92                        4.32e-09 ***
## DaysF96                        4.99e-09 ***
## DaysF99                         < 2e-16 ***
## DaysF103                        < 2e-16 ***
## DaysF106                        < 2e-16 ***
## DaysF110                        < 2e-16 ***
## SppO.fav                       3.59e-08 ***
## SppS.sid                       3.71e-13 ***
## TreatmentN:DaysF8              0.022519 *  
## TreatmentN+P:DaysF8            0.071933 .  
## TreatmentN:DaysF14             0.496282    
## TreatmentN+P:DaysF14           0.190659    
## TreatmentN:DaysF21             0.000236 ***
## TreatmentN+P:DaysF21           0.023290 *  
## TreatmentN:DaysF28             0.000537 ***
## TreatmentN+P:DaysF28           0.000397 ***
## TreatmentN:DaysF49             2.18e-08 ***
## TreatmentN+P:DaysF49           2.39e-07 ***
## TreatmentN:DaysF65             0.000477 ***
## TreatmentN+P:DaysF65           3.20e-06 ***
## TreatmentN:DaysF71             9.79e-06 ***
## TreatmentN+P:DaysF71           0.018517 *  
## TreatmentN:DaysF76             1.58e-05 ***
## TreatmentN+P:DaysF76           0.001188 ** 
## TreatmentN:DaysF84             0.004964 ** 
## TreatmentN+P:DaysF84           0.001435 ** 
## TreatmentN:DaysF89             0.002972 ** 
## TreatmentN+P:DaysF89           0.017926 *  
## TreatmentN:DaysF92             0.744578    
## TreatmentN+P:DaysF92           0.070946 .  
## TreatmentN:DaysF96             0.000382 ***
## TreatmentN+P:DaysF96           0.168662    
## TreatmentN:DaysF99              < 2e-16 ***
## TreatmentN+P:DaysF99           0.003420 ** 
## TreatmentN:DaysF103            4.85e-14 ***
## TreatmentN+P:DaysF103          1.36e-11 ***
## TreatmentN:DaysF106             < 2e-16 ***
## TreatmentN+P:DaysF106           < 2e-16 ***
## TreatmentN:DaysF110            7.55e-09 ***
## TreatmentN+P:DaysF110          1.36e-10 ***
## TreatmentN:SppO.fav            0.162010    
## TreatmentN+P:SppO.fav          0.179750    
## TreatmentN:SppS.sid            0.211509    
## TreatmentN+P:SppS.sid          0.971249    
## DaysF8:SppO.fav                0.382957    
## DaysF14:SppO.fav               0.029121 *  
## DaysF21:SppO.fav               0.101399    
## DaysF28:SppO.fav               0.868472    
## DaysF49:SppO.fav               0.161067    
## DaysF65:SppO.fav               0.006190 ** 
## DaysF71:SppO.fav               0.782608    
## DaysF76:SppO.fav               0.360491    
## DaysF84:SppO.fav               0.042049 *  
## DaysF89:SppO.fav               0.022837 *  
## DaysF92:SppO.fav               6.79e-05 ***
## DaysF96:SppO.fav               0.178566    
## DaysF99:SppO.fav               0.818305    
## DaysF103:SppO.fav              0.871697    
## DaysF106:SppO.fav              0.353303    
## DaysF110:SppO.fav              2.15e-13 ***
## DaysF8:SppS.sid                0.009689 ** 
## DaysF14:SppS.sid               7.13e-12 ***
## DaysF21:SppS.sid               0.010555 *  
## DaysF28:SppS.sid               3.67e-11 ***
## DaysF49:SppS.sid               2.08e-06 ***
## DaysF65:SppS.sid               1.15e-09 ***
## DaysF71:SppS.sid               4.57e-07 ***
## DaysF76:SppS.sid               3.09e-09 ***
## DaysF84:SppS.sid               6.46e-05 ***
## DaysF89:SppS.sid               0.002115 ** 
## DaysF92:SppS.sid               0.003785 ** 
## DaysF96:SppS.sid               0.001736 ** 
## DaysF99:SppS.sid               0.306757    
## DaysF103:SppS.sid              0.209807    
## DaysF106:SppS.sid              0.437188    
## DaysF110:SppS.sid               < 2e-16 ***
## TreatmentN:DaysF8:SppO.fav     0.220160    
## TreatmentN+P:DaysF8:SppO.fav   0.183367    
## TreatmentN:DaysF14:SppO.fav    0.208549    
## TreatmentN+P:DaysF14:SppO.fav  0.277633    
## TreatmentN:DaysF21:SppO.fav    0.038167 *  
## TreatmentN+P:DaysF21:SppO.fav  0.271678    
## TreatmentN:DaysF28:SppO.fav    0.247927    
## TreatmentN+P:DaysF28:SppO.fav  0.623823    
## TreatmentN:DaysF49:SppO.fav    0.064435 .  
## TreatmentN+P:DaysF49:SppO.fav  0.222771    
## TreatmentN:DaysF65:SppO.fav    0.000321 ***
## TreatmentN+P:DaysF65:SppO.fav  0.005119 ** 
## TreatmentN:DaysF71:SppO.fav    0.005418 ** 
## TreatmentN+P:DaysF71:SppO.fav  0.001774 ** 
## TreatmentN:DaysF76:SppO.fav    0.005042 ** 
## TreatmentN+P:DaysF76:SppO.fav  0.013268 *  
## TreatmentN:DaysF84:SppO.fav    0.037498 *  
## TreatmentN+P:DaysF84:SppO.fav  0.049823 *  
## TreatmentN:DaysF89:SppO.fav    0.003501 ** 
## TreatmentN+P:DaysF89:SppO.fav  0.131282    
## TreatmentN:DaysF92:SppO.fav    0.312131    
## TreatmentN+P:DaysF92:SppO.fav  0.007899 ** 
## TreatmentN:DaysF96:SppO.fav    0.045632 *  
## TreatmentN+P:DaysF96:SppO.fav  0.312365    
## TreatmentN:DaysF99:SppO.fav    0.000161 ***
## TreatmentN+P:DaysF99:SppO.fav  0.143965    
## TreatmentN:DaysF103:SppO.fav   0.000118 ***
## TreatmentN+P:DaysF103:SppO.fav 1.81e-05 ***
## TreatmentN:DaysF106:SppO.fav   8.67e-09 ***
## TreatmentN+P:DaysF106:SppO.fav 1.59e-06 ***
## TreatmentN:DaysF110:SppO.fav   7.51e-10 ***
## TreatmentN+P:DaysF110:SppO.fav 0.000762 ***
## TreatmentN:DaysF8:SppS.sid     0.929541    
## TreatmentN+P:DaysF8:SppS.sid   0.267413    
## TreatmentN:DaysF14:SppS.sid    0.403459    
## TreatmentN+P:DaysF14:SppS.sid  0.788218    
## TreatmentN:DaysF21:SppS.sid    0.858288    
## TreatmentN+P:DaysF21:SppS.sid  0.382361    
## TreatmentN:DaysF28:SppS.sid    0.778589    
## TreatmentN+P:DaysF28:SppS.sid  0.283043    
## TreatmentN:DaysF49:SppS.sid    0.010419 *  
## TreatmentN+P:DaysF49:SppS.sid  0.000405 ***
## TreatmentN:DaysF65:SppS.sid    7.44e-05 ***
## TreatmentN+P:DaysF65:SppS.sid  0.000223 ***
## TreatmentN:DaysF71:SppS.sid    0.001887 ** 
## TreatmentN+P:DaysF71:SppS.sid  0.080894 .  
## TreatmentN:DaysF76:SppS.sid    0.003134 ** 
## TreatmentN+P:DaysF76:SppS.sid  0.009107 ** 
## TreatmentN:DaysF84:SppS.sid    0.005029 ** 
## TreatmentN+P:DaysF84:SppS.sid  0.050764 .  
## TreatmentN:DaysF89:SppS.sid    0.108706    
## TreatmentN+P:DaysF89:SppS.sid  0.023365 *  
## TreatmentN:DaysF92:SppS.sid    0.077815 .  
## TreatmentN+P:DaysF92:SppS.sid  0.314545    
## TreatmentN:DaysF96:SppS.sid    7.30e-11 ***
## TreatmentN+P:DaysF96:SppS.sid  0.014002 *  
## TreatmentN:DaysF99:SppS.sid     < 2e-16 ***
## TreatmentN+P:DaysF99:SppS.sid  0.003946 ** 
## TreatmentN:DaysF103:SppS.sid    < 2e-16 ***
## TreatmentN+P:DaysF103:SppS.sid 6.69e-11 ***
## TreatmentN:DaysF106:SppS.sid    < 2e-16 ***
## TreatmentN+P:DaysF106:SppS.sid 3.65e-15 ***
## TreatmentN+P:DaysF110:SppS.sid 1.39e-10 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
       # plot(Effect(c("Treatment","Spp","DaysF"), LME1), x.var="DaysF", multiline=T, ci.style="bars",
       #    ylab="Fv/Fm", xlab="Days in nutient treatments")
    
      # EMMs
      All.YII.emm<-emmeans(LME1, ~Treatment * DaysF* Spp)
      emmip(LME1, ~DaysF|Treatment|Spp, CIs = TRUE) + theme_bw() + facet_grid(Spp~Treatment)

  # Spp responded differently, do separate analysis for each one

A.cer model

  LME_Acer<-lmerTest::lmer(YII ~ Treatment * DaysF + (1|Genotype/Fragment), 
                               data=subset(YII.data, Spp=="A.cer"), na.action=na.omit)
      summary(LME_Acer)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: YII ~ Treatment * DaysF + (1 | Genotype/Fragment)
##    Data: subset(YII.data, Spp == "A.cer")
## 
## REML criterion at convergence: -7076.6
## 
## Scaled residuals: 
##      Min       1Q   Median       3Q      Max 
## -14.5929  -0.4042   0.0553   0.4562   5.6395 
## 
## Random effects:
##  Groups            Name        Variance  Std.Dev.
##  Fragment:Genotype (Intercept) 0.0001250 0.01118 
##  Genotype          (Intercept) 0.0001976 0.01406 
##  Residual                      0.0005142 0.02268 
## Number of obs: 1619, groups:  Fragment:Genotype, 120; Genotype, 6
## 
## Fixed effects:
##                         Estimate Std. Error         df t value Pr(>|t|)
## (Intercept)            6.118e-01  7.053e-03  1.053e+01  86.741 2.23e-16
## TreatmentN            -1.124e-02  5.657e-03  1.015e+03  -1.986 0.047290
## TreatmentN+P          -6.843e-03  5.692e-03  1.014e+03  -1.202 0.229520
## DaysF8                -1.641e-03  5.135e-03  1.449e+03  -0.320 0.749330
## DaysF14                6.462e-03  5.135e-03  1.449e+03   1.258 0.208464
## DaysF21               -6.231e-03  5.135e-03  1.449e+03  -1.213 0.225167
## DaysF28               -1.144e-02  5.135e-03  1.449e+03  -2.227 0.026094
## DaysF49               -3.320e-02  5.135e-03  1.449e+03  -6.467 1.37e-10
## DaysF65               -4.377e-02  5.135e-03  1.449e+03  -8.524  < 2e-16
## DaysF71               -4.256e-02  5.135e-03  1.449e+03  -8.289 2.57e-16
## DaysF76               -5.182e-02  5.135e-03  1.449e+03 -10.092  < 2e-16
## DaysF84               -4.601e-02  5.429e-03  1.458e+03  -8.475  < 2e-16
## DaysF89               -6.429e-02  5.429e-03  1.458e+03 -11.843  < 2e-16
## DaysF92               -5.326e-02  5.429e-03  1.458e+03  -9.811  < 2e-16
## DaysF96               -5.304e-02  5.429e-03  1.458e+03  -9.771  < 2e-16
## DaysF99               -7.876e-02  5.429e-03  1.458e+03 -14.508  < 2e-16
## DaysF103              -9.810e-02  5.429e-03  1.458e+03 -18.071  < 2e-16
## DaysF106              -1.150e-01  5.429e-03  1.458e+03 -21.185  < 2e-16
## DaysF110              -2.122e-01  5.429e-03  1.458e+03 -39.093  < 2e-16
## TreatmentN:DaysF8      2.749e-02  7.173e-03  1.449e+03   3.833 0.000132
## TreatmentN+P:DaysF8    2.182e-02  7.216e-03  1.449e+03   3.023 0.002545
## TreatmentN:DaysF14     8.197e-03  7.173e-03  1.449e+03   1.143 0.253309
## TreatmentN+P:DaysF14   1.586e-02  7.216e-03  1.449e+03   2.198 0.028086
## TreatmentN:DaysF21     4.433e-02  7.173e-03  1.449e+03   6.180 8.31e-10
## TreatmentN+P:DaysF21   2.751e-02  7.216e-03  1.449e+03   3.812 0.000144
## TreatmentN:DaysF28     4.173e-02  7.173e-03  1.449e+03   5.818 7.33e-09
## TreatmentN+P:DaysF28   4.296e-02  7.216e-03  1.449e+03   5.953 3.29e-09
## TreatmentN:DaysF49     6.755e-02  7.173e-03  1.449e+03   9.417  < 2e-16
## TreatmentN+P:DaysF49   6.270e-02  7.216e-03  1.449e+03   8.689  < 2e-16
## TreatmentN:DaysF65     4.211e-02  7.173e-03  1.449e+03   5.871 5.36e-09
## TreatmentN+P:DaysF65   5.627e-02  7.241e-03  1.450e+03   7.770 1.47e-14
## TreatmentN:DaysF71     5.273e-02  7.248e-03  1.452e+03   7.276 5.63e-13
## TreatmentN+P:DaysF71   2.822e-02  7.241e-03  1.450e+03   3.897 0.000102
## TreatmentN:DaysF76     5.123e-02  7.275e-03  1.452e+03   7.041 2.93e-12
## TreatmentN+P:DaysF76   3.901e-02  7.241e-03  1.450e+03   5.387 8.33e-08
## TreatmentN:DaysF84     3.559e-02  7.801e-03  1.463e+03   4.562 5.48e-06
## TreatmentN+P:DaysF84   4.129e-02  7.733e-03  1.461e+03   5.339 1.08e-07
## TreatmentN:DaysF89     3.837e-02  7.847e-03  1.463e+03   4.890 1.12e-06
## TreatmentN+P:DaysF89   3.067e-02  7.733e-03  1.461e+03   3.966 7.67e-05
## TreatmentN:DaysF92    -5.437e-03  8.071e-03  1.465e+03  -0.674 0.500593
## TreatmentN+P:DaysF92   2.446e-02  7.863e-03  1.462e+03   3.110 0.001905
## TreatmentN:DaysF96    -4.797e-02  8.377e-03  1.467e+03  -5.727 1.24e-08
## TreatmentN+P:DaysF96  -1.997e-02  8.390e-03  1.466e+03  -2.380 0.017438
## TreatmentN:DaysF99    -1.156e-01  8.576e-03  1.468e+03 -13.482  < 2e-16
## TreatmentN+P:DaysF99  -4.191e-02  8.590e-03  1.467e+03  -4.879 1.18e-06
## TreatmentN:DaysF103   -1.112e-01  8.968e-03  1.469e+03 -12.400  < 2e-16
## TreatmentN+P:DaysF103 -9.820e-02  8.705e-03  1.467e+03 -11.280  < 2e-16
## TreatmentN:DaysF106   -1.810e-01  1.009e-02  1.473e+03 -17.929  < 2e-16
## TreatmentN+P:DaysF106 -1.426e-01  9.331e-03  1.470e+03 -15.285  < 2e-16
## TreatmentN+P:DaysF110 -1.302e-01  1.225e-02  1.476e+03 -10.630  < 2e-16
##                          
## (Intercept)           ***
## TreatmentN            *  
## TreatmentN+P             
## DaysF8                   
## DaysF14                  
## DaysF21                  
## DaysF28               *  
## DaysF49               ***
## DaysF65               ***
## DaysF71               ***
## DaysF76               ***
## DaysF84               ***
## DaysF89               ***
## DaysF92               ***
## DaysF96               ***
## DaysF99               ***
## DaysF103              ***
## DaysF106              ***
## DaysF110              ***
## TreatmentN:DaysF8     ***
## TreatmentN+P:DaysF8   ** 
## TreatmentN:DaysF14       
## TreatmentN+P:DaysF14  *  
## TreatmentN:DaysF21    ***
## TreatmentN+P:DaysF21  ***
## TreatmentN:DaysF28    ***
## TreatmentN+P:DaysF28  ***
## TreatmentN:DaysF49    ***
## TreatmentN+P:DaysF49  ***
## TreatmentN:DaysF65    ***
## TreatmentN+P:DaysF65  ***
## TreatmentN:DaysF71    ***
## TreatmentN+P:DaysF71  ***
## TreatmentN:DaysF76    ***
## TreatmentN+P:DaysF76  ***
## TreatmentN:DaysF84    ***
## TreatmentN+P:DaysF84  ***
## TreatmentN:DaysF89    ***
## TreatmentN+P:DaysF89  ***
## TreatmentN:DaysF92       
## TreatmentN+P:DaysF92  ** 
## TreatmentN:DaysF96    ***
## TreatmentN+P:DaysF96  *  
## TreatmentN:DaysF99    ***
## TreatmentN+P:DaysF99  ***
## TreatmentN:DaysF103   ***
## TreatmentN+P:DaysF103 ***
## TreatmentN:DaysF106   ***
## TreatmentN+P:DaysF106 ***
## TreatmentN+P:DaysF110 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
      Step.LME_Acer<-step (LME_Acer)
      final_fm <- get_model(Step.LME_Acer)
      summary(final_fm)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: YII ~ Treatment * DaysF + (1 | Genotype/Fragment)
##    Data: subset(YII.data, Spp == "A.cer")
## 
## REML criterion at convergence: -7076.6
## 
## Scaled residuals: 
##      Min       1Q   Median       3Q      Max 
## -14.5929  -0.4042   0.0553   0.4562   5.6395 
## 
## Random effects:
##  Groups            Name        Variance  Std.Dev.
##  Fragment:Genotype (Intercept) 0.0001250 0.01118 
##  Genotype          (Intercept) 0.0001976 0.01406 
##  Residual                      0.0005142 0.02268 
## Number of obs: 1619, groups:  Fragment:Genotype, 120; Genotype, 6
## 
## Fixed effects:
##                         Estimate Std. Error         df t value Pr(>|t|)
## (Intercept)            6.118e-01  7.053e-03  1.053e+01  86.741 2.23e-16
## TreatmentN            -1.124e-02  5.657e-03  1.015e+03  -1.986 0.047290
## TreatmentN+P          -6.843e-03  5.692e-03  1.014e+03  -1.202 0.229520
## DaysF8                -1.641e-03  5.135e-03  1.449e+03  -0.320 0.749330
## DaysF14                6.462e-03  5.135e-03  1.449e+03   1.258 0.208464
## DaysF21               -6.231e-03  5.135e-03  1.449e+03  -1.213 0.225167
## DaysF28               -1.144e-02  5.135e-03  1.449e+03  -2.227 0.026094
## DaysF49               -3.320e-02  5.135e-03  1.449e+03  -6.467 1.37e-10
## DaysF65               -4.377e-02  5.135e-03  1.449e+03  -8.524  < 2e-16
## DaysF71               -4.256e-02  5.135e-03  1.449e+03  -8.289 2.57e-16
## DaysF76               -5.182e-02  5.135e-03  1.449e+03 -10.092  < 2e-16
## DaysF84               -4.601e-02  5.429e-03  1.458e+03  -8.475  < 2e-16
## DaysF89               -6.429e-02  5.429e-03  1.458e+03 -11.843  < 2e-16
## DaysF92               -5.326e-02  5.429e-03  1.458e+03  -9.811  < 2e-16
## DaysF96               -5.304e-02  5.429e-03  1.458e+03  -9.771  < 2e-16
## DaysF99               -7.876e-02  5.429e-03  1.458e+03 -14.508  < 2e-16
## DaysF103              -9.810e-02  5.429e-03  1.458e+03 -18.071  < 2e-16
## DaysF106              -1.150e-01  5.429e-03  1.458e+03 -21.185  < 2e-16
## DaysF110              -2.122e-01  5.429e-03  1.458e+03 -39.093  < 2e-16
## TreatmentN:DaysF8      2.749e-02  7.173e-03  1.449e+03   3.833 0.000132
## TreatmentN+P:DaysF8    2.182e-02  7.216e-03  1.449e+03   3.023 0.002545
## TreatmentN:DaysF14     8.197e-03  7.173e-03  1.449e+03   1.143 0.253309
## TreatmentN+P:DaysF14   1.586e-02  7.216e-03  1.449e+03   2.198 0.028086
## TreatmentN:DaysF21     4.433e-02  7.173e-03  1.449e+03   6.180 8.31e-10
## TreatmentN+P:DaysF21   2.751e-02  7.216e-03  1.449e+03   3.812 0.000144
## TreatmentN:DaysF28     4.173e-02  7.173e-03  1.449e+03   5.818 7.33e-09
## TreatmentN+P:DaysF28   4.296e-02  7.216e-03  1.449e+03   5.953 3.29e-09
## TreatmentN:DaysF49     6.755e-02  7.173e-03  1.449e+03   9.417  < 2e-16
## TreatmentN+P:DaysF49   6.270e-02  7.216e-03  1.449e+03   8.689  < 2e-16
## TreatmentN:DaysF65     4.211e-02  7.173e-03  1.449e+03   5.871 5.36e-09
## TreatmentN+P:DaysF65   5.627e-02  7.241e-03  1.450e+03   7.770 1.47e-14
## TreatmentN:DaysF71     5.273e-02  7.248e-03  1.452e+03   7.276 5.63e-13
## TreatmentN+P:DaysF71   2.822e-02  7.241e-03  1.450e+03   3.897 0.000102
## TreatmentN:DaysF76     5.123e-02  7.275e-03  1.452e+03   7.041 2.93e-12
## TreatmentN+P:DaysF76   3.901e-02  7.241e-03  1.450e+03   5.387 8.33e-08
## TreatmentN:DaysF84     3.559e-02  7.801e-03  1.463e+03   4.562 5.48e-06
## TreatmentN+P:DaysF84   4.129e-02  7.733e-03  1.461e+03   5.339 1.08e-07
## TreatmentN:DaysF89     3.837e-02  7.847e-03  1.463e+03   4.890 1.12e-06
## TreatmentN+P:DaysF89   3.067e-02  7.733e-03  1.461e+03   3.966 7.67e-05
## TreatmentN:DaysF92    -5.437e-03  8.071e-03  1.465e+03  -0.674 0.500593
## TreatmentN+P:DaysF92   2.446e-02  7.863e-03  1.462e+03   3.110 0.001905
## TreatmentN:DaysF96    -4.797e-02  8.377e-03  1.467e+03  -5.727 1.24e-08
## TreatmentN+P:DaysF96  -1.997e-02  8.390e-03  1.466e+03  -2.380 0.017438
## TreatmentN:DaysF99    -1.156e-01  8.576e-03  1.468e+03 -13.482  < 2e-16
## TreatmentN+P:DaysF99  -4.191e-02  8.590e-03  1.467e+03  -4.879 1.18e-06
## TreatmentN:DaysF103   -1.112e-01  8.968e-03  1.469e+03 -12.400  < 2e-16
## TreatmentN+P:DaysF103 -9.820e-02  8.705e-03  1.467e+03 -11.280  < 2e-16
## TreatmentN:DaysF106   -1.810e-01  1.009e-02  1.473e+03 -17.929  < 2e-16
## TreatmentN+P:DaysF106 -1.426e-01  9.331e-03  1.470e+03 -15.285  < 2e-16
## TreatmentN+P:DaysF110 -1.302e-01  1.225e-02  1.476e+03 -10.630  < 2e-16
##                          
## (Intercept)           ***
## TreatmentN            *  
## TreatmentN+P             
## DaysF8                   
## DaysF14                  
## DaysF21                  
## DaysF28               *  
## DaysF49               ***
## DaysF65               ***
## DaysF71               ***
## DaysF76               ***
## DaysF84               ***
## DaysF89               ***
## DaysF92               ***
## DaysF96               ***
## DaysF99               ***
## DaysF103              ***
## DaysF106              ***
## DaysF110              ***
## TreatmentN:DaysF8     ***
## TreatmentN+P:DaysF8   ** 
## TreatmentN:DaysF14       
## TreatmentN+P:DaysF14  *  
## TreatmentN:DaysF21    ***
## TreatmentN+P:DaysF21  ***
## TreatmentN:DaysF28    ***
## TreatmentN+P:DaysF28  ***
## TreatmentN:DaysF49    ***
## TreatmentN+P:DaysF49  ***
## TreatmentN:DaysF65    ***
## TreatmentN+P:DaysF65  ***
## TreatmentN:DaysF71    ***
## TreatmentN+P:DaysF71  ***
## TreatmentN:DaysF76    ***
## TreatmentN+P:DaysF76  ***
## TreatmentN:DaysF84    ***
## TreatmentN+P:DaysF84  ***
## TreatmentN:DaysF89    ***
## TreatmentN+P:DaysF89  ***
## TreatmentN:DaysF92       
## TreatmentN+P:DaysF92  ** 
## TreatmentN:DaysF96    ***
## TreatmentN+P:DaysF96  *  
## TreatmentN:DaysF99    ***
## TreatmentN+P:DaysF99  ***
## TreatmentN:DaysF103   ***
## TreatmentN+P:DaysF103 ***
## TreatmentN:DaysF106   ***
## TreatmentN+P:DaysF106 ***
## TreatmentN+P:DaysF110 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## fit warnings:
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
      # EMMs
      Acer.YII.emm<-emmeans(LME_Acer, ~Treatment * DaysF)
      # contrast(Acer.YII.emm, "tukey")
      
      # Effect plot options
      emmip(LME_Acer, ~DaysF|Treatment, CIs = TRUE) + theme_bw() # interaction plot of predictions

      # Pairwise comparisons
      #pairs(Acer.YII.emm) # same than contrast(Acer.YII.emm, "tukey")
      
      #plot(emmeans(LME_Acer, ~DaysF|Treatment), comparisons = TRUE) +
      #  coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + facet_wrap(~Treatment) +
      #  theme_gdocs() # Tukey comparission (do not trust CI to compare EMMs)
      
      Acer.YII_groups<-cld(Acer.YII.emm, by=NULL) # compact-letter display
      Acer.YII_groups<-Acer.YII_groups[order(Acer.YII_groups$Day,Acer.YII_groups$Treatment),]
      Acer.YII_groups
##    Treatment DaysF    emmean          SE        df  lower.CL  upper.CL
## 1    Ambient     1 0.6117575 0.007054394 10.280294 0.5960972 0.6274178
## 2          N     1 0.6005227 0.006988574  9.910625 0.5849322 0.6161133
## 3        N+P     1 0.6049142 0.007013858 10.056684 0.5892982 0.6205301
## 4    Ambient     8 0.6101165 0.007054394 10.280294 0.5944562 0.6257768
## 5          N     8 0.6263764 0.006988574  9.910625 0.6107858 0.6419670
## 6        N+P     8 0.6250892 0.007013858 10.056684 0.6094732 0.6407051
## 7    Ambient    14 0.6182190 0.007054394 10.280294 0.6025588 0.6338793
## 8          N    14 0.6151813 0.006988574  9.910625 0.5995907 0.6307718
## 9        N+P    14 0.6272392 0.007013858 10.056684 0.6116232 0.6428551
## 10   Ambient    21 0.6055267 0.007054394 10.280294 0.5898665 0.6211870
## 11         N    21 0.6386203 0.006988574  9.910625 0.6230297 0.6542109
## 12       N+P    21 0.6261892 0.007013858 10.056684 0.6105732 0.6418051
## 13   Ambient    28 0.6003216 0.007054394 10.280294 0.5846613 0.6159819
## 14         N    28 0.6308154 0.006988574  9.910625 0.6152248 0.6464060
## 15       N+P    28 0.6364392 0.007013858 10.056684 0.6208232 0.6520551
## 16   Ambient    49 0.5785524 0.007054394 10.280294 0.5628921 0.5942127
## 17         N    49 0.6348642 0.006988574  9.910625 0.6192736 0.6504548
## 18       N+P    49 0.6344142 0.007013858 10.056684 0.6187982 0.6500301
## 19   Ambient    65 0.5679883 0.007054394 10.280294 0.5523280 0.5836486
## 20         N    65 0.5988642 0.006988574  9.910625 0.5832736 0.6144548
## 21       N+P    65 0.6174144 0.007040543 10.209743 0.6017706 0.6330581
## 22   Ambient    71 0.5691934 0.007054394 10.280294 0.5535331 0.5848537
## 23         N    71 0.6106904 0.007067800 10.365157 0.5950172 0.6263636
## 24       N+P    71 0.5905682 0.007040543 10.209743 0.5749245 0.6062120
## 25   Ambient    76 0.5599370 0.007054394 10.280294 0.5442767 0.5755973
## 26         N    76 0.5999320 0.007097383 10.538342 0.5842269 0.6156371
## 27       N+P    76 0.5921067 0.007040543 10.209743 0.5764630 0.6077504
## 28   Ambient    84 0.5657458 0.007268878 11.587312 0.5498455 0.5816462
## 29         N    84 0.5900989 0.007429536 12.646142 0.5740026 0.6061952
## 30       N+P    84 0.6001896 0.007334650 12.022479 0.5842121 0.6161671
## 31   Ambient    89 0.5474646 0.007268878 11.587312 0.5315643 0.5633649
## 32         N    89 0.5745990 0.007478144 12.979606 0.5584408 0.5907571
## 33       N+P    89 0.5712896 0.007334650 12.022479 0.5553121 0.5872671
## 34   Ambient    92 0.5584958 0.007268878 11.587312 0.5425955 0.5743962
## 35         N    92 0.5418237 0.007719437 14.719734 0.5253427 0.5583046
## 36       N+P    92 0.5761104 0.007473578 12.954230 0.5599589 0.5922619
## 37   Ambient    96 0.5587146 0.007268878 11.587312 0.5428143 0.5746149
## 38         N    96 0.4995058 0.008038734 17.297257 0.4825678 0.5164439
## 39       N+P    96 0.5319028 0.008031063 17.245374 0.5149771 0.5488285
## 40   Ambient    99 0.5329958 0.007268878 11.587312 0.5170955 0.5488962
## 41         N    99 0.4061401 0.008247991 19.157904 0.3888865 0.4233937
## 42       N+P    99 0.4842428 0.008243048 19.121014 0.4669973 0.5014883
## 43   Ambient   103 0.5136521 0.007268878 11.587312 0.4977518 0.5295524
## 44         N   103 0.3912216 0.008656211 23.208304 0.3733238 0.4091195
## 45       N+P   103 0.4086126 0.008364655 20.266143 0.3911790 0.4260463
## 46   Ambient   106 0.4967458 0.007268878 11.587312 0.4808455 0.5126462
## 47         N   106 0.3045293 0.009818955 38.201452 0.2846553 0.3244033
## 48       N+P   106 0.3472829 0.009014907 27.273710 0.3287946 0.3657713
## 49   Ambient   110 0.3995271 0.007268878 11.587312 0.3836268 0.4154274
## 50         N   110        NA          NA        NA        NA        NA
## 51       N+P   110 0.2624893 0.012008996 83.678289 0.2386067 0.2863718
##                       .group
## 1                   GHIJKL  
## 2                 EFGH      
## 3                   GHI     
## 4                   GHIJK   
## 5                     IJKLMN
## 6                     IJKLMN
## 7                    HIJKLMN
## 8                    HIJKLM 
## 9                      JKLMN
## 10                  GHIJ    
## 11                         N
## 12                     JKLMN
## 13                 FGH      
## 14                      KLMN
## 15                        MN
## 16           0ABCDE         
## 17                        MN
## 18                       LMN
## 19         890AB            
## 20                EFGH      
## 21                   HIJKLMN
## 22          90ABC           
## 23                  GHIJK   
## 24             BCDEFG       
## 25         890              
## 26                EFGH      
## 27              CDEFG       
## 28         890A             
## 29            ABCDEFG       
## 30               DEFGH      
## 31       6789               
## 32           0ABCD          
## 33          90ABC           
## 34        7890              
## 35       678                
## 36           0ABCDEF        
## 37        7890              
## 38     4                    
## 39      567                 
## 40      56                  
## 41    3                     
## 42     4                    
## 43     45                   
## 44    3                     
## 45    3                     
## 46     4                    
## 47  1                       
## 48   2                      
## 49    3                     
## 50                          
## 51  1
      write.csv(Acer.YII_groups, "Outputs/Multicomp_AcerYII.csv", row.names = F)

O.fav model

###### 
      # Ofav 
      LME_Ofav<-lmer(YII ~ Treatment * DaysF + (1|Genotype/Fragment), 
                     data=subset(YII.data, Spp=="O.fav"), na.action=na.omit)
      lmerTest::step (LME_Ofav)
## Backward reduced random-effect table:
## 
##                         Eliminated npar logLik     AIC    LRT Df
## <none>                               54 1915.5 -3722.9          
## (1 | Fragment:Genotype)          0   53 1866.7 -3627.5 97.422  1
## (1 | Genotype)                   0   53 1883.2 -3660.5 64.429  1
##                         Pr(>Chisq)    
## <none>                                
## (1 | Fragment:Genotype)  < 2.2e-16 ***
## (1 | Genotype)           1.001e-15 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Backward reduced fixed-effect table:
## Degrees of freedom method: Satterthwaite 
## 
##                 Eliminated  Sum Sq   Mean Sq NumDF  DenDF F value
## Treatment:DaysF          0 0.12191 0.0038097    32 867.62  5.2448
##                    Pr(>F)    
## Treatment:DaysF < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Model found:
## YII ~ Treatment * DaysF + (1 | Genotype/Fragment)
      summary(LME_Ofav)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: YII ~ Treatment * DaysF + (1 | Genotype/Fragment)
##    Data: subset(YII.data, Spp == "O.fav")
## 
## REML criterion at convergence: -3830.9
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -3.1623 -0.5974  0.0479  0.6430  2.4276 
## 
## Random effects:
##  Groups            Name        Variance  Std.Dev.
##  Fragment:Genotype (Intercept) 0.0001798 0.01341 
##  Genotype          (Intercept) 0.0006105 0.02471 
##  Residual                      0.0007264 0.02695 
## Number of obs: 983, groups:  Fragment:Genotype, 72; Genotype, 4
## 
## Fixed effects:
##                         Estimate Std. Error         df t value Pr(>|t|)
## (Intercept)            5.064e-01  1.380e-02  4.468e+00  36.702 1.03e-06
## TreatmentN             8.208e-03  8.690e-03  5.963e+02   0.945 0.345249
## TreatmentN+P           1.171e-02  8.690e-03  5.963e+02   1.347 0.178374
## DaysF8                -1.383e-02  7.780e-03  8.621e+02  -1.778 0.075756
## DaysF14                3.696e-02  7.780e-03  8.621e+02   4.750 2.38e-06
## DaysF21               -2.913e-02  7.780e-03  8.621e+02  -3.743 0.000194
## DaysF28               -1.375e-02  7.780e-03  8.621e+02  -1.767 0.077533
## DaysF49               -5.279e-02  7.780e-03  8.621e+02  -6.785 2.15e-11
## DaysF65               -5.500e-03  7.780e-03  8.621e+02  -0.707 0.479809
## DaysF71               -3.871e-02  7.780e-03  8.621e+02  -4.975 7.87e-07
## DaysF76               -3.904e-02  7.780e-03  8.621e+02  -5.018 6.34e-07
## DaysF84               -1.412e-02  8.765e-03  8.725e+02  -1.610 0.107671
## DaysF89               -2.868e-02  8.765e-03  8.725e+02  -3.272 0.001110
## DaysF92                9.563e-03  8.948e-03  8.735e+02   1.069 0.285445
## DaysF96               -7.277e-02  8.948e-03  8.735e+02  -8.133 1.43e-15
## DaysF99               -7.410e-02  8.948e-03  8.735e+02  -8.282 4.52e-16
## DaysF103              -9.450e-02  8.948e-03  8.735e+02 -10.562  < 2e-16
## DaysF106              -1.282e-01  9.149e-03  8.738e+02 -14.014  < 2e-16
## DaysF110              -9.172e-02  9.635e-03  8.739e+02  -9.519  < 2e-16
## TreatmentN:DaysF8      3.375e-03  1.100e-02  8.621e+02   0.307 0.759118
## TreatmentN+P:DaysF8   -4.417e-03  1.100e-02  8.621e+02  -0.401 0.688220
## TreatmentN:DaysF14    -1.654e-02  1.100e-02  8.621e+02  -1.503 0.133106
## TreatmentN+P:DaysF14  -5.542e-03  1.100e-02  8.621e+02  -0.504 0.614634
## TreatmentN:DaysF21     3.542e-03  1.100e-02  8.621e+02   0.322 0.747619
## TreatmentN+P:DaysF21   5.833e-03  1.100e-02  8.621e+02   0.530 0.596137
## TreatmentN:DaysF28     1.900e-02  1.100e-02  8.621e+02   1.727 0.084560
## TreatmentN+P:DaysF28   3.329e-02  1.100e-02  8.621e+02   3.026 0.002554
## TreatmentN:DaysF49     3.117e-02  1.100e-02  8.621e+02   2.833 0.004725
## TreatmentN+P:DaysF49   3.867e-02  1.100e-02  8.621e+02   3.514 0.000464
## TreatmentN:DaysF65    -2.871e-02  1.100e-02  8.621e+02  -2.609 0.009234
## TreatmentN+P:DaysF65   1.417e-03  1.100e-02  8.621e+02   0.129 0.897583
## TreatmentN:DaysF71    -1.083e-03  1.100e-02  8.621e+02  -0.098 0.921591
## TreatmentN+P:DaysF71  -3.308e-02  1.100e-02  8.621e+02  -3.007 0.002717
## TreatmentN:DaysF76    -2.708e-03  1.100e-02  8.621e+02  -0.246 0.805628
## TreatmentN+P:DaysF76  -9.458e-03  1.100e-02  8.621e+02  -0.860 0.390239
## TreatmentN:DaysF84    -7.511e-03  1.240e-02  8.725e+02  -0.606 0.544693
## TreatmentN+P:DaysF84   1.463e-03  1.240e-02  8.725e+02   0.118 0.906102
## TreatmentN:DaysF89    -2.342e-02  1.253e-02  8.731e+02  -1.870 0.061807
## TreatmentN+P:DaysF89   6.501e-04  1.240e-02  8.725e+02   0.052 0.958188
## TreatmentN:DaysF92    -2.684e-02  1.280e-02  8.742e+02  -2.097 0.036282
## TreatmentN+P:DaysF92  -3.208e-02  1.265e-02  8.735e+02  -2.535 0.011421
## TreatmentN:DaysF96    -4.006e-03  1.280e-02  8.742e+02  -0.313 0.754359
## TreatmentN+P:DaysF96   6.940e-03  1.280e-02  8.740e+02   0.542 0.587749
## TreatmentN:DaysF99    -3.117e-02  1.280e-02  8.742e+02  -2.436 0.015068
## TreatmentN+P:DaysF99  -6.276e-03  1.337e-02  8.750e+02  -0.469 0.638922
## TreatmentN:DaysF103   -2.270e-02  1.280e-02  8.742e+02  -1.774 0.076466
## TreatmentN+P:DaysF103  4.487e-03  1.337e-02  8.750e+02   0.336 0.737273
## TreatmentN:DaysF106   -3.712e-02  1.310e-02  8.746e+02  -2.833 0.004710
## TreatmentN+P:DaysF106 -2.553e-02  1.351e-02  8.753e+02  -1.890 0.059045
## TreatmentN:DaysF110   -7.150e-02  1.362e-02  8.753e+02  -5.248 1.93e-07
## TreatmentN+P:DaysF110 -3.448e-02  1.384e-02  8.759e+02  -2.492 0.012890
##                          
## (Intercept)           ***
## TreatmentN               
## TreatmentN+P             
## DaysF8                .  
## DaysF14               ***
## DaysF21               ***
## DaysF28               .  
## DaysF49               ***
## DaysF65                  
## DaysF71               ***
## DaysF76               ***
## DaysF84                  
## DaysF89               ** 
## DaysF92                  
## DaysF96               ***
## DaysF99               ***
## DaysF103              ***
## DaysF106              ***
## DaysF110              ***
## TreatmentN:DaysF8        
## TreatmentN+P:DaysF8      
## TreatmentN:DaysF14       
## TreatmentN+P:DaysF14     
## TreatmentN:DaysF21       
## TreatmentN+P:DaysF21     
## TreatmentN:DaysF28    .  
## TreatmentN+P:DaysF28  ** 
## TreatmentN:DaysF49    ** 
## TreatmentN+P:DaysF49  ***
## TreatmentN:DaysF65    ** 
## TreatmentN+P:DaysF65     
## TreatmentN:DaysF71       
## TreatmentN+P:DaysF71  ** 
## TreatmentN:DaysF76       
## TreatmentN+P:DaysF76     
## TreatmentN:DaysF84       
## TreatmentN+P:DaysF84     
## TreatmentN:DaysF89    .  
## TreatmentN+P:DaysF89     
## TreatmentN:DaysF92    *  
## TreatmentN+P:DaysF92  *  
## TreatmentN:DaysF96       
## TreatmentN+P:DaysF96     
## TreatmentN:DaysF99    *  
## TreatmentN+P:DaysF99     
## TreatmentN:DaysF103   .  
## TreatmentN+P:DaysF103    
## TreatmentN:DaysF106   ** 
## TreatmentN+P:DaysF106 .  
## TreatmentN:DaysF110   ***
## TreatmentN+P:DaysF110 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
      # EMMs
      Ofav.YII.emm<-emmeans(LME_Ofav, ~Treatment * DaysF)
      # contrast(Ofav.YII.emm, "tukey")
      
      # Effect plot options
      emmip(LME_Ofav, ~DaysF|Treatment, CIs = TRUE) + theme_gdocs() # interaction plot of predictions

      # Pairwise comparisons
      #pairs(Ofav.YII.emm) # same than contrast(Acer.YII.emm, "tukey")
      
      # Pairwise comparisons
      plot(emmeans(LME_Ofav, ~DaysF|Treatment), comparisons = TRUE) +
        coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) +
        facet_wrap(~Treatment) +
        theme_bw() # Tukey comparission (do not trust CI to compare EMMs)

      Ofav.YII_groups<-cld(Ofav.YII.emm, by=NULL) # compact-letter display
      Ofav.YII_groups<-Ofav.YII_groups[order(Ofav.YII_groups$Day,Ofav.YII_groups$Treatment),]
      Ofav.YII_groups
##    Treatment DaysF    emmean         SE       df  lower.CL  upper.CL
## 1    Ambient     1 0.5064167 0.01379815 4.471946 0.4696499 0.5431835
## 2          N     1 0.5146250 0.01379815 4.471946 0.4778582 0.5513918
## 3        N+P     1 0.5181250 0.01379815 4.471946 0.4813582 0.5548918
## 4    Ambient     8 0.4925833 0.01379815 4.471946 0.4558165 0.5293501
## 5          N     8 0.5041667 0.01379815 4.471946 0.4673999 0.5409335
## 6        N+P     8 0.4998750 0.01379815 4.471946 0.4631082 0.5366418
## 7    Ambient    14 0.5433750 0.01379815 4.471946 0.5066082 0.5801418
## 8          N    14 0.5350417 0.01379815 4.471946 0.4982749 0.5718085
## 9        N+P    14 0.5495417 0.01379815 4.471946 0.5127749 0.5863085
## 10   Ambient    21 0.4772917 0.01379815 4.471946 0.4405249 0.5140585
## 11         N    21 0.4890417 0.01379815 4.471946 0.4522749 0.5258085
## 12       N+P    21 0.4948333 0.01379815 4.471946 0.4580665 0.5316001
## 13   Ambient    28 0.4926667 0.01379815 4.471946 0.4558999 0.5294335
## 14         N    28 0.5198750 0.01379815 4.471946 0.4831082 0.5566418
## 15       N+P    28 0.5376667 0.01379815 4.471946 0.5008999 0.5744335
## 16   Ambient    49 0.4536250 0.01379815 4.471946 0.4168582 0.4903918
## 17         N    49 0.4930000 0.01379815 4.471946 0.4562332 0.5297668
## 18       N+P    49 0.5040000 0.01379815 4.471946 0.4672332 0.5407668
## 19   Ambient    65 0.5009167 0.01379815 4.471946 0.4641499 0.5376835
## 20         N    65 0.4804167 0.01379815 4.471946 0.4436499 0.5171835
## 21       N+P    65 0.5140417 0.01379815 4.471946 0.4772749 0.5508085
## 22   Ambient    71 0.4677083 0.01379815 4.471946 0.4309415 0.5044751
## 23         N    71 0.4748333 0.01379815 4.471946 0.4380665 0.5116001
## 24       N+P    71 0.4463333 0.01379815 4.471946 0.4095665 0.4831001
## 25   Ambient    76 0.4673750 0.01379815 4.471946 0.4306082 0.5041418
## 26         N    76 0.4728750 0.01379815 4.471946 0.4361082 0.5096418
## 27       N+P    76 0.4696250 0.01379815 4.471946 0.4328582 0.5063918
## 28   Ambient    84 0.4923014 0.01437743 5.269204 0.4559038 0.5286990
## 29         N    84 0.4929983 0.01437743 5.269204 0.4566008 0.5293959
## 30       N+P    84 0.5054723 0.01437743 5.269204 0.4690747 0.5418699
## 31   Ambient    89 0.4777389 0.01437743 5.269204 0.4413413 0.5141365
## 32         N    89 0.4625228 0.01449003 5.435763 0.4261554 0.4988901
## 33       N+P    89 0.4900973 0.01437743 5.269204 0.4536997 0.5264949
## 34   Ambient    92 0.5159799 0.01448951 5.434999 0.4796125 0.5523473
## 35         N    92 0.4973489 0.01461734 5.628795 0.4610019 0.5336959
## 36       N+P    92 0.4956130 0.01448951 5.434999 0.4592456 0.5319805
## 37   Ambient    96 0.4336466 0.01448951 5.434999 0.3972792 0.4700140
## 38         N    96 0.4378489 0.01461734 5.628795 0.4015019 0.4741959
## 39       N+P    96 0.4522952 0.01461626 5.627189 0.4159482 0.4886422
## 40   Ambient    99 0.4323132 0.01448951 5.434999 0.3959458 0.4686807
## 41         N    99 0.4093489 0.01461734 5.628795 0.3730019 0.4456959
## 42       N+P    99 0.4377452 0.01512243 6.445708 0.4013534 0.4741370
## 43   Ambient   103 0.4119132 0.01448951 5.434999 0.3755458 0.4482807
## 44         N   103 0.3974203 0.01461734 5.628795 0.3610733 0.4337673
## 45       N+P   103 0.4281088 0.01512243 6.445708 0.3917171 0.4645006
## 46   Ambient   106 0.3782053 0.01461499 5.625295 0.3418582 0.4145523
## 47         N   106 0.3492897 0.01476106 5.852906 0.3129495 0.3856298
## 48       N+P   106 0.3643816 0.01512243 6.445708 0.3279898 0.4007734
## 49   Ambient   110 0.4147013 0.01492391 6.115019 0.3783497 0.4510530
## 50         N   110 0.3514105 0.01492677 6.119543 0.3150583 0.3877628
## 51       N+P   110 0.3919270 0.01512243 6.445708 0.3555352 0.4283188
##                       .group
## 1                  FGHIJKL  
## 2                     IJKLMN
## 3                      JKLM 
## 4              BCDEFGHIJ    
## 5                 E GHIJKL  
## 6              BCDEFGHIJ    
## 7                         MN
## 8                       KLMN
## 9                          N
## 10         890ABCDEFG       
## 11            ABCDEFGHIJ    
## 12             BCDEFGHIJ    
## 13             BCDEFGHIJ    
## 14                     JKLMN
## 15                       LMN
## 16       67890              
## 17             BCDEFGHIJ    
## 18                 FGHIJK   
## 19              C EFGHIJK   
## 20          90ABCDEFGH      
## 21                   HIJKLM 
## 22       67890AB D          
## 23          90ABCDEFG       
## 24      56789               
## 25       67890AB D          
## 26         890ABCD F        
## 27        7890ABC E         
## 28            ABCDEFGHIJ    
## 29            ABCDEFGHIJ    
## 30               D FGHIJKLM 
## 31         890ABCDEFGHI     
## 32       67890ABC           
## 33           0ABCDEFGHIJ    
## 34                   HIJKLMN
## 35             BCDEFGHIJ    
## 36             BCDEFGHIJ    
## 37     4567                 
## 38     45678                
## 39      567890A             
## 40     4567                 
## 41   2345                   
## 42     456789               
## 43    345                   
## 44   234                    
## 45     456                  
## 46  123                     
## 47  1                       
## 48  12                      
## 49    345                   
## 50  1                       
## 51  1234
      write.csv(Ofav.YII_groups, "Outputs/Multicomp_OfavYII.csv", row.names = F)

Ssid model

LME_Ssid<-lmer(YII ~ Treatment * DaysF + (1|Genotype/Fragment), 
                     REML=TRUE, data=subset(YII.data, Spp=="S.sid"),
                      na.action=na.omit)
      step (LME_Ssid)
## Backward reduced random-effect table:
## 
##                         Eliminated npar logLik     AIC    LRT Df
## <none>                               54 3774.8 -7441.7          
## (1 | Fragment:Genotype)          0   53 3759.5 -7412.9 30.718  1
## (1 | Genotype)                   0   53 3730.7 -7355.5 88.185  1
##                         Pr(>Chisq)    
## <none>                                
## (1 | Fragment:Genotype)  2.983e-08 ***
## (1 | Genotype)           < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Backward reduced fixed-effect table:
## Degrees of freedom method: Satterthwaite 
## 
##                 Eliminated  Sum Sq  Mean Sq NumDF  DenDF F value    Pr(>F)
## Treatment:DaysF          0 0.39611 0.012379    32 2205.3  5.8963 < 2.2e-16
##                    
## Treatment:DaysF ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Model found:
## YII ~ Treatment * DaysF + (1 | Genotype/Fragment)
      summary(LME_Ssid)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: YII ~ Treatment * DaysF + (1 | Genotype/Fragment)
##    Data: subset(YII.data, Spp == "S.sid")
## 
## REML criterion at convergence: -7549.7
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -6.3946 -0.4867  0.0610  0.6196  2.6395 
## 
## Random effects:
##  Groups            Name        Variance  Std.Dev.
##  Fragment:Genotype (Intercept) 0.0001237 0.01112 
##  Genotype          (Intercept) 0.0003108 0.01763 
##  Residual                      0.0020994 0.04582 
## Number of obs: 2414, groups:  Fragment:Genotype, 162; Genotype, 7
## 
## Fixed effects:
##                         Estimate Std. Error         df t value Pr(>|t|)
## (Intercept)            4.668e-01  9.250e-03  2.069e+01  50.458  < 2e-16
## TreatmentN            -2.529e-02  9.033e-03  2.231e+03  -2.800 0.005157
## TreatmentN+P          -7.407e-03  9.117e-03  2.231e+03  -0.812 0.416604
## DaysF8                 2.765e-02  8.818e-03  2.194e+03   3.135 0.001738
## DaysF14                8.424e-02  8.818e-03  2.194e+03   9.553  < 2e-16
## DaysF21                2.272e-02  8.818e-03  2.194e+03   2.577 0.010035
## DaysF28                6.363e-02  8.818e-03  2.194e+03   7.216 7.34e-13
## DaysF49                2.057e-02  8.818e-03  2.194e+03   2.333 0.019726
## DaysF65                2.521e-02  8.861e-03  2.196e+03   2.845 0.004483
## DaysF71                1.457e-02  8.861e-03  2.197e+03   1.645 0.100184
## DaysF76                1.538e-02  8.861e-03  2.197e+03   1.736 0.082666
## DaysF84                2.149e-03  9.659e-03  2.234e+03   0.222 0.823973
## DaysF89               -2.731e-02  9.659e-03  2.234e+03  -2.828 0.004728
## DaysF92               -1.844e-02  9.659e-03  2.234e+03  -1.909 0.056352
## DaysF96               -9.124e-02  9.659e-03  2.234e+03  -9.446  < 2e-16
## DaysF99               -9.139e-02  9.659e-03  2.234e+03  -9.462  < 2e-16
## DaysF103              -1.135e-01  9.659e-03  2.234e+03 -11.756  < 2e-16
## DaysF106              -1.247e-01  9.659e-03  2.234e+03 -12.908  < 2e-16
## DaysF110              -9.567e-02  9.659e-03  2.234e+03  -9.905  < 2e-16
## TreatmentN:DaysF8      2.890e-02  1.241e-02  2.194e+03   2.328 0.020008
## TreatmentN+P:DaysF8    3.954e-02  1.253e-02  2.194e+03   3.156 0.001622
## TreatmentN:DaysF14     2.145e-02  1.241e-02  2.194e+03   1.728 0.084134
## TreatmentN+P:DaysF14   1.157e-02  1.253e-02  2.194e+03   0.924 0.355846
## TreatmentN:DaysF21     4.150e-02  1.241e-02  2.194e+03   3.343 0.000843
## TreatmentN+P:DaysF21   4.147e-02  1.253e-02  2.194e+03   3.310 0.000949
## TreatmentN:DaysF28     4.619e-02  1.241e-02  2.194e+03   3.721 0.000204
## TreatmentN+P:DaysF28   2.580e-02  1.253e-02  2.194e+03   2.060 0.039557
## TreatmentN:DaysF49     2.690e-02  1.241e-02  2.194e+03   2.167 0.030351
## TreatmentN+P:DaysF49   6.143e-03  1.253e-02  2.194e+03   0.490 0.623974
## TreatmentN:DaysF65    -2.066e-02  1.244e-02  2.195e+03  -1.660 0.096961
## TreatmentN+P:DaysF65  -2.271e-03  1.259e-02  2.196e+03  -0.180 0.856865
## TreatmentN:DaysF71     4.335e-03  1.244e-02  2.196e+03   0.348 0.727577
## TreatmentN+P:DaysF71   8.038e-04  1.256e-02  2.196e+03   0.064 0.948976
## TreatmentN:DaysF76     5.597e-03  1.244e-02  2.196e+03   0.450 0.652928
## TreatmentN+P:DaysF76  -2.234e-03  1.256e-02  2.196e+03  -0.178 0.858843
## TreatmentN:DaysF84    -1.148e-02  1.353e-02  2.232e+03  -0.848 0.396344
## TreatmentN+P:DaysF84   7.540e-03  1.363e-02  2.231e+03   0.553 0.580292
## TreatmentN:DaysF89     1.142e-02  1.353e-02  2.232e+03   0.844 0.398890
## TreatmentN+P:DaysF89  -8.473e-03  1.363e-02  2.231e+03  -0.622 0.534332
## TreatmentN:DaysF92     2.667e-02  1.353e-02  2.232e+03   1.971 0.048895
## TreatmentN+P:DaysF92   6.155e-03  1.363e-02  2.231e+03   0.451 0.651720
## TreatmentN:DaysF96     6.744e-02  1.353e-02  2.232e+03   4.983 6.74e-07
## TreatmentN+P:DaysF96   2.480e-02  1.363e-02  2.231e+03   1.819 0.069048
## TreatmentN:DaysF99     5.942e-02  1.353e-02  2.232e+03   4.391 1.18e-05
## TreatmentN+P:DaysF99   1.053e-02  1.363e-02  2.231e+03   0.772 0.440057
## TreatmentN:DaysF103    7.831e-02  1.353e-02  2.232e+03   5.786 8.22e-09
## TreatmentN+P:DaysF103  2.183e-02  1.363e-02  2.231e+03   1.601 0.109443
## TreatmentN:DaysF106    5.500e-02  1.353e-02  2.232e+03   4.064 5.00e-05
## TreatmentN+P:DaysF106  7.411e-03  1.363e-02  2.231e+03   0.544 0.586811
## TreatmentN:DaysF110    6.507e-02  1.353e-02  2.232e+03   4.808 1.63e-06
## TreatmentN+P:DaysF110  1.869e-02  1.363e-02  2.231e+03   1.371 0.170659
##                          
## (Intercept)           ***
## TreatmentN            ** 
## TreatmentN+P             
## DaysF8                ** 
## DaysF14               ***
## DaysF21               *  
## DaysF28               ***
## DaysF49               *  
## DaysF65               ** 
## DaysF71                  
## DaysF76               .  
## DaysF84                  
## DaysF89               ** 
## DaysF92               .  
## DaysF96               ***
## DaysF99               ***
## DaysF103              ***
## DaysF106              ***
## DaysF110              ***
## TreatmentN:DaysF8     *  
## TreatmentN+P:DaysF8   ** 
## TreatmentN:DaysF14    .  
## TreatmentN+P:DaysF14     
## TreatmentN:DaysF21    ***
## TreatmentN+P:DaysF21  ***
## TreatmentN:DaysF28    ***
## TreatmentN+P:DaysF28  *  
## TreatmentN:DaysF49    *  
## TreatmentN+P:DaysF49     
## TreatmentN:DaysF65    .  
## TreatmentN+P:DaysF65     
## TreatmentN:DaysF71       
## TreatmentN+P:DaysF71     
## TreatmentN:DaysF76       
## TreatmentN+P:DaysF76     
## TreatmentN:DaysF84       
## TreatmentN+P:DaysF84     
## TreatmentN:DaysF89       
## TreatmentN+P:DaysF89     
## TreatmentN:DaysF92    *  
## TreatmentN+P:DaysF92     
## TreatmentN:DaysF96    ***
## TreatmentN+P:DaysF96  .  
## TreatmentN:DaysF99    ***
## TreatmentN+P:DaysF99     
## TreatmentN:DaysF103   ***
## TreatmentN+P:DaysF103    
## TreatmentN:DaysF106   ***
## TreatmentN+P:DaysF106    
## TreatmentN:DaysF110   ***
## TreatmentN+P:DaysF110    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
      # EMMs
      Ssid.YII.emm<-emmeans(LME_Ssid, ~Treatment * DaysF)
      # contrast(Ssid.YII.emm, "tukey")
      
      # Effect plot options
      emmip(LME_Ssid, ~DaysF|Treatment, CIs = TRUE) + theme_gdocs() # interaction plot of predictions

      # Pairwise comparisons
      # pairs(Ssid.YII.emm) # same than contrast(Ssid.YII.emm, "tukey")
      
      # Tukey comparission (do not trust CI to compare EMMs)
      plot(emmeans(LME_Ssid, ~DaysF|Treatment), comparisons = TRUE) +
        coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + facet_wrap(~Treatment) +
        theme_gdocs()

      Ssid.YII_groups<-cld(Ssid.YII.emm, by=NULL) # compact-letter display
      Ssid.YII_groups<-Ssid.YII_groups[order(Ssid.YII_groups$Day,Ssid.YII_groups$Treatment),]
      Ssid.YII_groups
##    Treatment DaysF    emmean          SE       df  lower.CL  upper.CL
## 1    Ambient     1 0.4667566 0.009250378 20.66614 0.4475004 0.4860127
## 2          N     1 0.4414666 0.009209706 20.30662 0.4222741 0.4606591
## 3        N+P     1 0.4593494 0.009292842 21.04607 0.4400264 0.4786723
## 4    Ambient     8 0.4944047 0.009250378 20.66614 0.4751485 0.5136609
## 5          N     8 0.4980121 0.009209706 20.30662 0.4788195 0.5172046
## 6        N+P     8 0.5265381 0.009292842 21.04607 0.5072151 0.5458610
## 7    Ambient    14 0.5509973 0.009250378 20.66614 0.5317411 0.5702534
## 8          N    14 0.5471575 0.009209706 20.30662 0.5279650 0.5663501
## 9        N+P    14 0.5551607 0.009292842 21.04607 0.5358378 0.5744837
## 10   Ambient    21 0.4894788 0.009250378 20.66614 0.4702226 0.5087349
## 11         N    21 0.5056848 0.009209706 20.30662 0.4864923 0.5248773
## 12       N+P    21 0.5235381 0.009292842 21.04607 0.5042151 0.5428610
## 13   Ambient    28 0.5303862 0.009250378 20.66614 0.5111300 0.5496423
## 14         N    28 0.5512848 0.009209706 20.30662 0.5320923 0.5704773
## 15       N+P    28 0.5487834 0.009292842 21.04607 0.5294604 0.5681063
## 16   Ambient    49 0.4873306 0.009250378 20.66614 0.4680745 0.5065868
## 17         N    49 0.4889393 0.009209706 20.30662 0.4697468 0.5081319
## 18       N+P    49 0.4860664 0.009292842 21.04607 0.4667434 0.5053893
## 19   Ambient    65 0.4919649 0.009291166 21.03123 0.4726446 0.5112852
## 20         N    65 0.4460121 0.009209706 20.30662 0.4268195 0.4652046
## 21       N+P    65 0.4822866 0.009334978 21.42846 0.4628970 0.5016761
## 22   Ambient    71 0.4813301 0.009291639 21.03540 0.4620091 0.5006511
## 23         N    71 0.4603757 0.009209706 20.30662 0.4411832 0.4795682
## 24       N+P    71 0.4747267 0.009292842 21.04607 0.4554038 0.4940497
## 25   Ambient    76 0.4821414 0.009291639 21.03540 0.4628204 0.5014625
## 26         N    76 0.4624484 0.009209706 20.30662 0.4432559 0.4816410
## 27       N+P    76 0.4725003 0.009292842 21.04607 0.4531774 0.4918233
## 28   Ambient    84 0.4689052 0.010055888 28.80008 0.4483324 0.4894780
## 29         N    84 0.4321341 0.009918204 27.26565 0.4117929 0.4524753
## 30       N+P    84 0.4690381 0.009986807 28.02280 0.4485818 0.4894944
## 31   Ambient    89 0.4394437 0.010055888 28.80008 0.4188709 0.4600165
## 32         N    89 0.4255732 0.009918204 27.26565 0.4052320 0.4459144
## 33       N+P    89 0.4235631 0.009986807 28.02280 0.4031068 0.4440194
## 34   Ambient    92 0.4483155 0.010055888 28.80008 0.4277427 0.4688883
## 35         N    92 0.4496951 0.009918204 27.26565 0.4293539 0.4700363
## 36       N+P    92 0.4470631 0.009986807 28.02280 0.4266068 0.4675194
## 37   Ambient    96 0.3755206 0.010055888 28.80008 0.3549478 0.3960934
## 38         N    96 0.4176707 0.009918204 27.26565 0.3973295 0.4380119
## 39       N+P    96 0.3929131 0.009986807 28.02280 0.3724568 0.4133694
## 40   Ambient    99 0.3753668 0.010055888 28.80008 0.3547940 0.3959396
## 41         N    99 0.4095000 0.009918204 27.26565 0.3891588 0.4298412
## 42       N+P    99 0.3784881 0.009986807 28.02280 0.3580318 0.3989444
## 43   Ambient   103 0.3532129 0.010055888 28.80008 0.3326401 0.3737857
## 44         N   103 0.4062317 0.009918204 27.26565 0.3858905 0.4265729
## 45       N+P   103 0.3676381 0.009986807 28.02280 0.3471818 0.3880944
## 46   Ambient   106 0.3420847 0.010055888 28.80008 0.3215119 0.3626575
## 47         N   106 0.3717927 0.009918204 27.26565 0.3514515 0.3921339
## 48       N+P   106 0.3420881 0.009986807 28.02280 0.3216318 0.3625444
## 49   Ambient   110 0.3710847 0.010055888 28.80008 0.3505119 0.3916575
## 50         N   110 0.4108658 0.009918204 27.26565 0.3905246 0.4312070
## 51       N+P   110 0.3823631 0.009986807 28.02280 0.3619068 0.4028194
##                    .group
## 1            0ABCDEF     
## 2         7890A          
## 3           90ABCDE      
## 4                 EFGHI  
## 5                  FGHIJ 
## 6                     IJK
## 7                       K
## 8                       K
## 9                       K
## 10                EFGH   
## 11                  GHIJ 
## 12                   HIJK
## 13                     JK
## 14                      K
## 15                      K
## 16               DEFGH   
## 17                EFGH   
## 18              CDEFG    
## 19                EFGHI  
## 20         890AB         
## 21             BCDEFG    
## 22             BCDEFG    
## 23          90ABCDE      
## 24            ABCDEFG    
## 25             BCDEFG    
## 26          90ABCDE      
## 27            ABCDEFG    
## 28           0ABCDEFG    
## 29       67890           
## 30           0ABCDEFG    
## 31        7890A          
## 32       6789            
## 33       6789            
## 34        7890ABC        
## 35         890ABCD       
## 36        7890AB         
## 37  12345                
## 38      5678             
## 39   23456               
## 40  1234                 
## 41    345678             
## 42  12345                
## 43  12                   
## 44    34567              
## 45  123                  
## 46  1                    
## 47  1234                 
## 48  1                    
## 49  1234                 
## 50     45678             
## 51  12345
      write.csv(Ssid.YII_groups, "Outputs/Multicomp_SsidYII.csv", row.names = F)

Only nutrients

############################################################          
 ################### ONLY NUTRIENT PHASE ##################
############################################################
          
# Select data for Nutrient enrichment (26C) only
      
    # Raw YII data              
    YII_Colony<- ggplot(YII.nutrients, aes (Days, YII, colour=Genotype)) +
      stat_summary(fun.data = "mean_cl_boot",geom = "errorbar", width = 0.2 )+
      stat_summary(fun.y=mean, geom="line") +   theme_gdocs()
    YII_Colony + ylim(0.0, 0.65) + facet_grid (Spp~Treatment)

    YII_Fragm<- ggplot(YII.nutrients, aes (Days, YII, colour=Treatment)) +
      stat_summary(fun.data = "mean_cl_boot",geom = "errorbar", width = 0.2 )+
      stat_summary(fun.y=mean, geom="line") +   ggthe_bw
    YII_Fragm + ylim(0.25, 0.65) + facet_wrap (Spp~Genotype)

    YII_Trea<- ggplot(YII.nutrients, aes (Days, YII, colour=factor(Treatment))) +
      stat_summary(fun.data = "mean_cl_boot",geom = "errorbar",
                   position = position_dodge(width = 1), width = 0.2 )+
      stat_summary(fun.y=mean, geom="line") +
      facet_grid (~Spp) + theme_gdocs()+
      scale_x_continuous(name="Days in nutrient treatment",
                         breaks=c(seq(-30,76, by=15))) +
      ylab("Fv/Fm") + ylim(0.01, 0.65)

    YII_Trea + guides(colour=guide_legend("Treatment"))+
      theme(legend.position=c(0.15, 0.3),
            plot.background=element_blank(),
            legend.box.background = element_rect())